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cnvnator patch #503

Merged
merged 5 commits into from
Jan 31, 2024
Merged

cnvnator patch #503

merged 5 commits into from
Jan 31, 2024

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ramprasadn
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PR checklist

CNVnator processes rewrite the input file so it nextflow's -resume could never work. This PR patches cnvnator module to circumvent this issue.

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jan 31, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit c530f9d

+| ✅ 176 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - docs/images/nf-core-raredisease_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-raredisease_logo_dark.png does not match the template

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.12
  • Run at 2024-01-31 15:19:39

@ramprasadn ramprasadn marked this pull request as ready for review January 31, 2024 10:43
jemten
jemten approved these changes Jan 31, 2024
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👍

@ramprasadn ramprasadn merged commit 6c1962d into nf-core:dev Jan 31, 2024
5 of 6 checks passed
@ramprasadn ramprasadn deleted the cnvnator-test branch February 2, 2024 16:56
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@jemten jemten jemten approved these changes

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@ramprasadn @jemten